Import Main Dataset

## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

Total Bovine Copy Numbers

## `summarise()` regrouping output by 'VariableKit' (override with `.groups` argument)
## `summarise()` regrouping output by 'VariableSpikeSet' (override with `.groups` argument)
##    VariableSpikeSet VariableKit     mean     st_dev n_failures n_total
## 1             First     COREDNA 5.510743 0.05437988          0       6
## 2             First      EZFood 5.023606 0.07381508          0       6
## 3             First    Mastitis 5.337045 0.05887863          0       6
## 4             First       Pfood 4.875976 0.05016906          0       6
## 5             First      PSoilP 3.832946 0.11231042          0       6
## 6             First   PviralDNA 5.226245 0.05143839          0       6
## 7             First     ZymoDNA 4.830652 0.05446231          0       6
## 8            Second     COREDNA 5.396342 0.07460889          0       6
## 9            Second    Mastitis 5.394293 0.02064839          0       6
## 10           Second       Pfood 4.775180 0.03994283          0       6
## 11           Second      PSoilP 4.084926 0.19020018          0       6
## 12           Second   PviralDNA 5.085082 0.08519742          0       6
## 13           Second     ZymoDNA 4.785882 0.03169048          0       6
## 14            Third     COREDNA 5.435192 0.07802399          0       6
## 15            Third      EZFood 4.391762 0.72817640          0       6
## 16            Third    Mastitis 5.364249 0.06220550          0       6
## 17            Third       Pfood 4.939664 0.02942455          0       6
## 18            Third      PSoilP 4.232332 0.22067912          0       6
## 19            Third   PviralDNA 5.286011 0.07253691          0       6
## 20            Third     ZymoDNA 4.814657 0.09134190          0       6
## Warning: Removed 80 rows containing missing values (geom_point).

Total Bacterial DNA

## 
## Attaching package: 'wrangle'
## The following object is masked from 'package:dplyr':
## 
##     group_by_all
## `summarise()` regrouping output by 'VariableKit' (override with `.groups` argument)
## `summarise()` regrouping output by 'VariableSpikeSet' (override with `.groups` argument)
##    VariableSpikeSet VariableKit     mean     st_dev n_failures n_total
## 1             First     COREDNA 6.565413 0.05259444          0       6
## 2             First      EZFood 4.277616 1.45768760          0       6
## 3             First    Mastitis 6.805970 0.01589447          0       6
## 4             First       Pfood 6.076956 0.02287900          0       6
## 5             First      PSoilP 5.698609 0.11744216          0       6
## 6             First   PviralDNA 6.192312 0.03599713          0       6
## 7             First     ZymoDNA 6.346418 0.03366165          0       6
## 8            Second     COREDNA 7.490835 0.02140125          0       6
## 9            Second    Mastitis 7.668798 0.02543933          0       6
## 10           Second       Pfood 6.631503 0.04452933          0       6
## 11           Second      PSoilP 6.439095 0.15846125          0       6
## 12           Second   PviralDNA 7.121062 0.07745249          0       6
## 13           Second     ZymoDNA 6.697743 0.04461625          0       6
## 14            Third     COREDNA 6.881582 1.74763906          1       6
## 15            Third      EZFood 4.342899 2.30314702          2       6
## 16            Third    Mastitis 8.053032 0.06686248          0       6
## 17            Third       Pfood 7.418800 0.03041420          0       6
## 18            Third      PSoilP 6.795545 0.08899794          0       6
## 19            Third   PviralDNA 7.556803 0.10432742          0       6
## 20            Third     ZymoDNA 7.282966 0.12384595          0       6
## Warning: Removed 22 rows containing missing values (geom_point).

## Warning: Removed 3 rows containing missing values (geom_point).

## Warning: Removed 3 rows containing missing values (geom_point).

Bacillus wiedmannii Copy Numbers

## `summarise()` regrouping output by 'VariableKit' (override with `.groups` argument)
## `summarise()` regrouping output by 'VariableSpikeSet' (override with `.groups` argument)
##    VariableSpikeSet VariableKit     mean     st_dev n_failures n_total
## 1             First     COREDNA 6.126799 0.05946479          0       6
## 2             First      EZFood 4.199089 0.99412039          1       6
## 3             First    Mastitis 6.541652 0.02719433          0       6
## 4             First       Pfood 5.417196 0.92199266          0       6
## 5             First      PSoilP 5.311014 0.18316303          0       6
## 6             First   PviralDNA 5.518817 0.08786240          0       6
## 7             First     ZymoDNA 6.028139 0.03599635          0       6
## 8            Second     COREDNA 6.433043 0.09141025          0       6
## 9            Second    Mastitis 6.469291 0.01607210          0       6
## 10           Second       Pfood 5.662830 0.08101734          0       6
## 11           Second      PSoilP 5.317932 0.17244727          0       6
## 12           Second   PviralDNA 6.091386 0.08779476          0       6
## 13           Second     ZymoDNA 5.641826 0.02664997          0       6
## 14            Third     COREDNA 7.019606 0.02640080          0       6
## 15            Third      EZFood 4.500444 0.18655080          3       6
## 16            Third    Mastitis 7.012577 0.04008723          0       6
## 17            Third       Pfood 6.400803 0.03383823          1       6
## 18            Third      PSoilP 6.186386 0.12209311          0       6
## 19            Third   PviralDNA 6.674293 0.07478131          0       6
## 20            Third     ZymoDNA 6.397461 0.09433067          0       6
## Warning: Removed 87 rows containing missing values (geom_point).

## Warning: Removed 5 rows containing missing values (geom_point).

## Warning: Removed 5 rows containing missing values (geom_point).

Listeria monocytogenes Copy Numbers

## `summarise()` regrouping output by 'VariableKit' (override with `.groups` argument)
## `summarise()` regrouping output by 'VariableSpikeSet' (override with `.groups` argument)
##    VariableSpikeSet VariableKit     mean     st_dev n_failures n_total
## 1             First     COREDNA 4.996165 0.07118535          0       6
## 2             First      EZFood      NaN         NA          6       6
## 3             First    Mastitis 5.920458 0.03284588          0       6
## 4             First       Pfood 5.261206 0.05882789          0       6
## 5             First      PSoilP 4.589896 0.10368861          1       6
## 6             First   PviralDNA      NaN         NA          6       6
## 7             First     ZymoDNA 5.217074 0.10607334          0       6
## 8            Second     COREDNA 6.764514 0.06440611          0       6
## 9            Second    Mastitis 6.925829 0.05305144          0       6
## 10           Second       Pfood 6.209820 0.05854870          0       6
## 11           Second      PSoilP 5.652350 0.28801610          2       6
## 12           Second   PviralDNA 6.818189 0.10167286          0       6
## 13           Second     ZymoDNA 6.299305 0.06699653          0       6
## 14            Third     COREDNA 6.868625 0.03112356          0       6
## 15            Third      EZFood      NaN         NA          6       6
## 16            Third    Mastitis 6.906907 0.01320150          0       6
## 17            Third       Pfood 6.311089 0.02199862          0       6
## 18            Third      PSoilP 6.058299 0.11216514          0       6
## 19            Third   PviralDNA 6.871705 0.08573938          0       6
## 20            Third     ZymoDNA 6.483661 0.19226732          0       6
## Warning: Removed 130 rows containing missing values (geom_point).

## Warning: Removed 21 rows containing missing values (geom_point).

## Warning: Removed 21 rows containing missing values (geom_point).

Mycobacterium smegmatis Copy Numbers

## `summarise()` regrouping output by 'VariableKit' (override with `.groups` argument)
## `summarise()` regrouping output by 'VariableSpikeSet' (override with `.groups` argument)
##    VariableSpikeSet VariableKit     mean     st_dev n_failures n_total
## 1             First     COREDNA 6.410321 0.03379999          0       6
## 2             First      EZFood 3.387637 0.53911986          2       6
## 3             First    Mastitis 6.132651 0.03721685          0       6
## 4             First       Pfood 5.835527 0.02840872          0       6
## 5             First      PSoilP 4.337075 0.18166318          0       6
## 6             First   PviralDNA 5.791533 0.06735908          0       6
## 7             First     ZymoDNA 5.517488 0.08926898          0       6
## 8            Second     COREDNA 7.101812 0.07093623          0       6
## 9            Second    Mastitis 7.079584 0.02215197          0       6
## 10           Second       Pfood 6.579458 0.04582864          0       6
## 11           Second      PSoilP 6.072664 0.17450050          0       6
## 12           Second   PviralDNA 6.680003 0.03305596          0       6
## 13           Second     ZymoDNA 6.701950 0.04422551          0       6
## 14            Third     COREDNA 6.917894 0.08192923          0       6
## 15            Third      EZFood 6.308042         NA          5       6
## 16            Third    Mastitis 6.875300 0.03405437          0       6
## 17            Third       Pfood 6.465286 0.02810963          0       6
## 18            Third      PSoilP 5.904056 0.13596609          0       6
## 19            Third   PviralDNA 6.266574 0.08559028          0       6
## 20            Third     ZymoDNA 6.695051 0.19000457          0       6
## Warning: Removed 101 rows containing missing values (geom_point).

## Warning: Removed 7 rows containing missing values (geom_point).

## Warning: Removed 7 rows containing missing values (geom_point).

Salmonella sp. Copy Numbers

## `summarise()` regrouping output by 'VariableKit' (override with `.groups` argument)
## `summarise()` regrouping output by 'VariableSpikeSet' (override with `.groups` argument)
##    VariableSpikeSet VariableKit     mean     st_dev n_failures n_total
## 1             First     COREDNA 6.021926 0.03689540          0       6
## 2             First      EZFood 3.553886 0.92148645          0       6
## 3             First    Mastitis 5.055847 0.05638093          0       6
## 4             First       Pfood 4.427881 0.02807177          0       6
## 5             First      PSoilP 3.313556 0.16097627          0       6
## 6             First   PviralDNA 5.637821 0.04113447          0       6
## 7             First     ZymoDNA 4.600919 0.09323729          0       6
## 8            Second     COREDNA 5.819654 0.08889109          0       6
## 9            Second    Mastitis 5.855133 0.01505745          0       6
## 10           Second       Pfood 5.161440 0.07302418          0       6
## 11           Second      PSoilP 4.265153 0.24970082          0       6
## 12           Second   PviralDNA 5.648986 0.06073656          0       6
## 13           Second     ZymoDNA 5.412725 0.02695026          0       6
## 14            Third     COREDNA 6.381353 0.15232282          0       6
## 15            Third      EZFood 5.491051         NA          5       6
## 16            Third    Mastitis 6.491253 0.03059223          0       6
## 17            Third       Pfood 6.136920 0.04606326          0       6
## 18            Third      PSoilP 5.157145 0.08449168          2       6
## 19            Third   PviralDNA 6.017032 0.10019394          0       6
## 20            Third     ZymoDNA 6.011617 0.20713085          0       6
## Warning: Removed 100 rows containing missing values (geom_point).

## Warning: Removed 7 rows containing missing values (geom_point).

## Warning: Removed 7 rows containing missing values (geom_point).